[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 --- Comment #15 from Fedora Update System upda...@fedoraproject.org 2011-07-12 11:00:07 EDT --- mmseq-0.9.11-1.el5 has been pushed to the Fedora EPEL 5 stable repository. -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 Fedora Update System upda...@fedoraproject.org changed: What|Removed |Added Status|ON_QA |CLOSED Fixed In Version||mmseq-0.9.11-1.el5 Resolution||ERRATA Last Closed||2011-07-12 11:00:14 -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 Fedora Update System upda...@fedoraproject.org changed: What|Removed |Added Status|MODIFIED|ON_QA --- Comment #14 from Fedora Update System upda...@fedoraproject.org 2011-06-21 13:13:46 EDT --- mmseq-0.9.11-1.el5 has been pushed to the Fedora EPEL 5 testing repository. -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 Fedora Update System upda...@fedoraproject.org changed: What|Removed |Added Status|ON_QA |MODIFIED -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 --- Comment #13 from Fedora Update System upda...@fedoraproject.org 2011-06-17 11:26:52 EDT --- mmseq-0.9.11-1.el5 has been submitted as an update for Fedora EPEL 5. https://admin.fedoraproject.org/updates/mmseq-0.9.11-1.el5 -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 Adam Huffman bl...@verdurin.com changed: What|Removed |Added Status|NEW |ON_QA -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 Adam Huffman bl...@verdurin.com changed: What|Removed |Added Flag||fedora-cvs? --- Comment #11 from Adam Huffman bl...@verdurin.com 2011-05-29 10:42:26 EDT --- New Package SCM Request === Package Name: mmseq Short Description: Haplotype and isoform specific expression estimation for RNA-seq Owners: verdurin Branches: f14 f15 el5 el6 InitialCC: -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 --- Comment #12 from Jason Tibbitts ti...@math.uh.edu 2011-05-29 11:21:42 EDT --- Git done (by process-git-requests). -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 --- Comment #9 from Adam Huffman bl...@verdurin.com 2011-05-28 06:23:11 EDT --- New upstream release: http://verdurin.fedorapeople.org/reviews/mmseq/mmseq.spec http://verdurin.fedorapeople.org/reviews/mmseq/mmseq-0.9.11-1.fc16.src.rpm I've reminded the upstream author about the incorrect FSF addresses. -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 Volker Fröhlich volke...@gmx.at changed: What|Removed |Added Flag|fedora-review? |fedora-review+ --- Comment #10 from Volker Fröhlich volke...@gmx.at 2011-05-28 09:47:53 EDT --- As the name issue is solved, the package is fine. md5sum: 6c75e6866eb702b7b22892b63340280e http://koji.fedoraproject.org/koji/taskinfo?taskID=3097653 APPROVED -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 --- Comment #7 from Adam Huffman bl...@verdurin.com 2011-05-27 10:13:59 EDT --- New version at: http://verdurin.fedorapeople.org/reviews/mmseq/mmseq.spec http://verdurin.fedorapeople.org/reviews/mmseq/mmseq-0.9.10b-3.fc16.src.rpm I patched the Makefile as you suggested but without the zlib-devel BR builds in Mock failed. I will be building for EPEL and samtools will be there soon (I maintain the EPEL branches). The upstream author explained that 0.9.10b is a post-release update, which according to the guidelines at http://fedoraproject.org/wiki/PackageNamingGuidelines#NonNumericRelease is acceptable as is. I've removed VERSION. -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 --- Comment #8 from Adam Huffman bl...@verdurin.com 2011-05-27 10:24:12 EDT --- The wrong version was uploaded - I've fixed that now. -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=697836
--- Comment #4 from Volker Fröhlich volke...@gmx.at 2011-05-14 05:55:08 EDT
---
The naming guidelines are not met for this pre-release version. Please see the
review below for details and correct it.
Concerning the current FSF address, please see
https://bugzilla.redhat.com/show_bug.cgi?id=690919#c5
It is not considered as a blocker, so it is up to you.
Please correct the VERSION file prior building, as it contains the wrong
version number. I'd also exclude it from the file section, as it serves no use
as far as I can see.
I'd prefer having a new line for every BuildRequires, as it is clearer. You can
also be more specific on the script file names in the files section.
If you don't plan to introduce the package into EPEL, you can drop the clean
section, the rm -rf %{buildroot} and the BuildRoot definition. It seems like,
there are no samtools in EPEL yet.
Remove the extra white-space in front of the word Example.
I'm not sure if zlib is used at all. It's in the flags, but I can't see how
they'd use it. This might not be important.
Review:
[+] Good
[-] Needs work
[0] Does not apply
MUST:
=
[+] rpmlint:
[makerpm@fedora14 mmseq_0.9.10b]$ rpmlint
/var/lib/mock/fedora-rawhide-x86_64/result/mmseq-*
mmseq.src: W: spelling-error Summary(en_US) Haplotype - Haplology, Holotype,
Haplography
mmseq.src: W: spelling-error Summary(en_US) isoform - iodoform, isomorph,
proforma
mmseq.src: W: spelling-error %description -l en_US haplotype - haplology,
holotype, haplography
mmseq.src: W: spelling-error %description -l en_US isoform - iodoform,
isomorph, proforma
mmseq.src: W: spelling-error %description -l en_US multi - mulch, mufti
mmseq.x86_64: W: spelling-error Summary(en_US) Haplotype - Haplology,
Holotype, Haplography
mmseq.x86_64: W: spelling-error Summary(en_US) isoform - iodoform, isomorph,
proforma
mmseq.x86_64: W: spelling-error %description -l en_US haplotype - haplology,
holotype, haplography
mmseq.x86_64: W: spelling-error %description -l en_US isoform - iodoform,
isomorph, proforma
mmseq.x86_64: W: spelling-error %description -l en_US multi - mulch, mufti
mmseq.x86_64: E: incorrect-fsf-address /usr/bin/testregexp.rb
mmseq.x86_64: E: incorrect-fsf-address /usr/bin/sam2hits.rb
mmseq.x86_64: E: incorrect-fsf-address /usr/bin/filterGTF.rb
mmseq.x86_64: E: incorrect-fsf-address /usr/bin/fastagrep.sh
mmseq.x86_64: E: incorrect-fsf-address /usr/bin/haploref.rb
mmseq.x86_64: W: no-manual-page-for-binary haploref.rb
mmseq.x86_64: W: no-manual-page-for-binary ensembl_gtf_to_gff.pl
mmseq.x86_64: W: no-manual-page-for-binary mmseq
mmseq.x86_64: W: no-manual-page-for-binary get_isize.rb
mmseq.x86_64: W: no-manual-page-for-binary bam2hits
mmseq.x86_64: W: no-manual-page-for-binary fastagrep.sh
mmseq.x86_64: W: no-manual-page-for-binary filterGTF.rb
mmseq.x86_64: W: no-manual-page-for-binary sam2hits.rb
mmseq.x86_64: W: no-manual-page-for-binary testregexp.rb
mmseq.x86_64: W: no-manual-page-for-binary pileup.sh
mmseq-debuginfo.x86_64: E: incorrect-fsf-address
/usr/src/debug/mmseq_0.9.10b/mmseq.cpp
mmseq-debuginfo.x86_64: E: incorrect-fsf-address
/usr/src/debug/mmseq_0.9.10b/sokal.cc
3 packages and 0 specfiles checked; 7 errors, 20 warnings.
[-] Naming according to the Package Naming Guidelines: Please see
http://fedoraproject.org/wiki/PackageNamingGuidelines#NonNumericRelease
[+] Spec file matches base package name
[+] Packaging guidelines met
[+] License approved for Fedora
[+] License field in spec matches code
[+] License file included, if source package includes it
[+] Spec in American English
[+] Spec is legible
[+] Sources match upstream md5sum: 1f1c5b338eec23994fd84edb7e00b17a
[+] Compiles and builds into binary RPMs on at least one primary architecture:
http://koji.fedoraproject.org/koji/taskinfo?taskID=3071848
[0] ExcludeArch is specified and commented
[0] Locales are handled correctly
[+] All build dependencies listed
[0] Calls ldconfig for its shared libraries
[+] No bundled system libraries
[0] Stated as relocatable package
[+] Owns all its directories or requires package that does
[+] No file listing duplicates
[+] File permissions correct
[+] Consistent use of macros
[+] Code or permissible content
[0] Large documentation in -doc subpackage
[+] No runtime dependency of files listed as %doc
[0] Header files in -devel subpackage
[0] Static files in -static subpackage
[0] Library files without suffix in -devel subpackage
[0] Devel-package requires base package
[0] No .la libtool archives
[0] GUI application includes properly installed %{name}.desktop file
[+] No files or directories owned, that other packages own
[+] Filenames in packages are UTF-8
SHOULD:
===
[0] Query upstream if no license text is included
[+] Package builds in mock: Tried fedora-rawhide-x86_64,
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 --- Comment #5 from Volker Fröhlich volke...@gmx.at 2011-05-14 09:44:06 EDT --- Replacing -lz with -Wl,--as-needed -lz proves right: zlib is unnecessary. You can drop from the BRs and remove it from the Makefile. -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 --- Comment #6 from Volker Fröhlich volke...@gmx.at 2011-05-14 15:01:13 EDT --- Please also delete the 4 pre-built binaries in the prep section! http://fedoraproject.org/wiki/Packaging/Guidelines#No_inclusion_of_pre-built_binaries_or_libraries -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 --- Comment #3 from Adam Huffman bl...@verdurin.com 2011-05-13 19:41:32 EDT --- The upstream developer has said he'll fix the FSF address problems in the next release. -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 Volker Fröhlich volke...@gmx.at changed: What|Removed |Added AssignedTo|nob...@fedoraproject.org|volke...@gmx.at Flag||fedora-review? -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 --- Comment #2 from Adam Huffman bl...@verdurin.com 2011-05-08 08:01:13 EDT --- (In reply to comment #1) Just some comments: Thanks for looking Please include the license file. The postal addresses of the FSF are outdated in several files. File included and I'll contact upstream about the out of data FSF address. Use -p on the install commands, at least for the scripts. One of the scripts uses the samtools binary, so you'll need an explicit Require on that, as RPM will only install samtools-libs Done. Besides the first part of the package description is pretty generic, it says, it would contain instructions. I can't see any and especially the mmseq binary is especially sparse on saying anything. Why does the description not have the word Haplotype? I was trying to differentiate the description from the summary but have improved it now. Why did you choose to not install the Perl script? Fixed. You might want to add -b .name_of_the_patch to the patch macros. Please also comment on the patches. Done. I've also updated to the latest upstream release. http://verdurin.fedorapeople.org/reviews/mmseq/mmseq.spec http://verdurin.fedorapeople.org/reviews/mmseq/mmseq-0.9.10b-1.fc16.src.rpm -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug. https://bugzilla.redhat.com/show_bug.cgi?id=697836 Volker Fröhlich volke...@gmx.at changed: What|Removed |Added CC||volke...@gmx.at --- Comment #1 from Volker Fröhlich volke...@gmx.at 2011-05-06 18:44:39 EDT --- Just some comments: Please include the license file. The postal addresses of the FSF are outdated in several files. Use -p on the install commands, at least for the scripts. One of the scripts uses the samtools binary, so you'll need an explicit Require on that, as RPM will only install samtools-libs Besides the first part of the package description is pretty generic, it says, it would contain instructions. I can't see any and especially the mmseq binary is especially sparse on saying anything. Why does the description not have the word Haplotype? Why did you choose to not install the Perl script? You might want to add -b .name_of_the_patch to the patch macros. Please also comment on the patches. -- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the bug. ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
